LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 # For Simulator : LAMMPS 12 Dec 2018 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.15999 3.15999 3.15999 Created orthogonal box = (0 -40.2232 0) to (9.47996 40.2232 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.26665 4.4689 4.4689 Created 109 atoms create_atoms CPU = 0.000207901 secs 109 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.26665 4.4689 4.4689 Created 109 atoms create_atoms CPU = 7.00951e-05 secs 109 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXIKJvEG/Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXIKJvEG/Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 3 25 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 214 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4771.5378 0 -4771.5378 13778.652 26 0 -4784.3273 0 -4784.3273 -729.69422 Loop time of 1.51425 on 1 procs for 26 steps with 214 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4771.53778869 -4784.32379007 -4784.32729425 Force two-norm initial, final = 29.7179 0.181452 Force max component initial, final = 9.28464 0.0396541 Final line search alpha, max atom move = 1 0.0396541 Iterations, force evaluations = 26 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5127 | 1.5127 | 1.5127 | 0.0 | 99.90 Neigh | 0.000525 | 0.000525 | 0.000525 | 0.0 | 0.03 Comm | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004127 | | | 0.03 Nlocal: 214 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1861 ave 1861 max 1861 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13724 ave 13724 max 13724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13724 Ave neighs/atom = 64.1308 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -4784.3273 0 -4784.3273 -729.69422 3408.1152 28 0 -4784.3385 0 -4784.3385 4223.7253 3401.7282 Loop time of 0.146818 on 1 procs for 2 steps with 214 atoms 102.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4784.32729425 -4784.33817142 -4784.33849891 Force two-norm initial, final = 16.7522 1.08394 Force max component initial, final = 13.7966 0.992566 Final line search alpha, max atom move = 0.000537393 0.000533398 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14662 | 0.14662 | 0.14662 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.3167e-05 | 5.3167e-05 | 5.3167e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000144 | | | 0.10 Nlocal: 214 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1867 ave 1867 max 1867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13712 ave 13712 max 13712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13712 Ave neighs/atom = 64.0748 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.229 | 4.229 | 4.229 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4784.3385 0 -4784.3385 4223.7253 Loop time of 9.53674e-07 on 1 procs for 0 steps with 214 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 214 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1867 ave 1867 max 1867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13712 ave 13712 max 13712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13712 Ave neighs/atom = 64.0748 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.229 | 4.229 | 4.229 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4784.3385 -4784.3385 9.4745411 80.446487 4.4630766 4223.7253 4223.7253 467.21998 12018.971 184.98521 2.5299778 185.19093 Loop time of 9.53674e-07 on 1 procs for 0 steps with 214 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 214 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1867 ave 1867 max 1867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6856 ave 6856 max 6856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13712 ave 13712 max 13712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13712 Ave neighs/atom = 64.0748 Neighbor list builds = 0 Dangerous builds = 0 214 -1087.31818906068 eV 2.52997780334872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01